Most metagenomic vanT calls are not vancomycin resistance genes

Metagenomic resistome surveys frequently report vanTG as the dominant glycopeptide resistance gene, but these calls rely on homology without verifying catalytic residues or operon context. By analyzing 107,008 metagenome-assembled genomes, we demonstrate that only 3.7% of predicted vanTG genes possess the required active-site substitution, with the vast majority being misannotated alanine racemases. Incorporating structural and genomic context corrections reveals a novel split-architecture lineage in gut-associated Erysipelotrichales missed by current profiling tools.